Collapsible modular genomic pipeline

Abstract

The invention generally relates to tools for genomic analysis and particularly to a pipeline editor that can turn pipelines into standalone tools for use in other pipelines. The invention provides systems and methods for genomic analysis in which individual analytical tools can be arranged into analytical pipelines that can then be “collapsed” into standalone tools, which themselves can be put into the pool of individual tools for use in further building of pipelines. Aspects of the invention provide a system that includes a server computer system operable to present to a user a plurality of genomic tools, receive input from the user arranging the tools into a pipeline, create a new tool that includes the pipeline, and offer the new tool along with the plurality of genomic tools.

What is claimed is: 
     
         1 . A system for genomic analysis, the system comprising:
 a server computer system comprising a processor coupled to a memory operable to cause the system to:
 present to a user a plurality of genomic tools; 
 receive input from the user arranging the tools into a pipeline; 
 create a new tool that includes the pipeline; and 
 offer the new tool along with the plurality of genomic tools. 
   
     
     
         2 . The system of  claim 1 , wherein each of the plurality of genomic tools and the new tool is presented using an icon displayed in a web browser on a user computer device connected to the server computer system. 
     
     
         3 . The system of  claim 1 , wherein the input arranging the tools includes dragging and dropping the tools within a graphical interface. 
     
     
         4 . The system of  claim 1 , further operable by the user to:
 create an additional pipeline that includes the new tool;   create an additional tool that includes the additional pipeline; and   offer the plurality of genomic tools, the new tool, and the additional tool for arrangement into genomic pipelines by displaying an icon for each.   
     
     
         5 . The system of  claim 1 , wherein:
 a first one of the plurality of genomic tools is operable to obtain nucleotide sequence data from sequence read files,   a second one of the plurality of genomic tools is operable to align nucleotide sequence data, and   a third one of the plurality of genomic tools is operable to compare sequence reads to a reference   
     
     
         6 . The system of  claim 1 , further operable to:
 receive nucleotide sequence data from a remote source computer;   instruct a remote cloud computer to use the plurality of genomic tools to analyze the nucleotide sequence data; and   deliver output genomic information to a remote user computer.   
     
     
         7 . The system of  claim 1 , further operable to execute the new tool in response to a user clicking a link within a document on a remote user computer. 
     
     
         8 . The system of  claim 7 , further operable to execute the new tool in response to a second user clicking the link within the document after the document has been transferred to a different computer. 
     
     
         9 . The system of  claim 1 , wherein offering the new tool along with the plurality of genomic tools comprises:
 representing each of the plurality of genomic tools using an icon in a graphical pipeline editor on a user terminal;   representing the new tool using a new icon in the graphical pipeline editor, the new icon clickable to execute the pipeline; and   providing the graphical pipeline editor for the user to use to arrange the icons into a different pipeline.   
     
     
         10 . The system of  claim 9 , further operable to represent inputs and outputs of tools graphically, and to represent inputs and outputs of pipelines in the same way that inputs and outputs of tools are represented. 
     
     
         11 . A method for genomic analysis, the method comprising:
 using a computer system comprising a processor coupled to a memory to:
 present to a user a plurality of genomic tools; 
 receive input from the user arranging the tools into a pipeline; 
 create a new tool that includes the pipeline; and 
 offer the new tool along with the plurality of genomic tools. 
   
     
     
         12 . The method of  claim 11 , wherein each of the plurality of genomic tools and the new tool is presented using an icon displayed in a web browser. 
     
     
         13 . The method of  claim 11 , wherein the input arranging the tools includes dragging and dropping the tools within a graphical interface. 
     
     
         14 . The method of  claim 11 , further comprising using the computer system to:
 create an additional pipeline that includes the new tool;   create an additional tool that includes the additional pipeline; and   offer the plurality of genomic tools, the new tool, and the additional tool for arrangement into genomic pipelines.   
     
     
         15 . The method of  claim 11 , wherein:
 a first one of the plurality of genomic tools is operable to obtain nucleotide sequence data from sequence read files,   a second one of the plurality of genomic tools is operable to align nucleotide sequence data, and   a third one of the plurality of genomic tools is operable to compare sequence reads to a reference   
     
     
         16 . The method of  claim 11 , further comprising using the computer system to:
 receive nucleotide sequence data;   instruct a remote cloud computer to use the plurality of genomic tools to analyze the nucleotide sequence data; and   provide output genomic information.   
     
     
         17 . The method of  claim 11 , further comprising:
 representing each of the plurality of tools using an icon in a pipeline editor on a user terminal;   representing the new tool using a new icon in the pipeline editor; and   providing the pipeline editor for the user to use to arrange the icons into a different pipeline.   
     
     
         18 . The method of  claim 17 , wherein the computer system operable to represent inputs and outputs of tools graphically, and to represent inputs and outputs of pipelines in the same way that inputs and outputs of tools are represented. 
     
     
         19 . A system for genomic analysis, the system comprising:
 a processor coupled to a memory containing instructions operable to cause the system to present a user interface that presents a plurality of tools, the user interface operable by a user to:
 assemble individual ones of the plurality of tools into a pipeline; 
 create a new pipeline tool that provides the same functionality as the pipeline; and 
 present the new pipeline tool along with the plurality of tools. 
   
     
     
         20 . The system of  claim 19 , wherein each of the plurality of tools and the new pipeline tool comprises instructions operable to cause the system to receive a predetermined genomic data input, change the genomic data input, and output new genomic data. 
     
     
         21 . The system of  claim 19 , wherein the user interface comprises a display including an icon for each tool that can be dragged and dropped into a pipeline area of the display. 
     
     
         22 . The system of  claim 21 , wherein each icon can be connected to at least one other icon by a user to cause the system to use the connected tools to analyze genomic data. 
     
     
         23 . The system of  claim 19 , wherein creating the new pipeline tool comprises creating instructions that route input data to the first tool in the pipeline, and through the subsequent tools in the pipeline. 
     
     
         24 . The system of  claim 21 , wherein presenting the new pipeline tool includes displaying an icon for the tool that can be dragged into the pipeline area. 
     
     
         25 . The system of  claim 24 , wherein any of the pipeline tools, including the new pipeline tool, can be linked to any one or more of each other to create other pipeline. 
     
     
         26 . The system of  claim 25 , further operable to store the other pipelines as new tools within the plurality of tools. 
     
     
         27 . The system of  claim 19 , further operable to execute the pipeline upon receiving a request initiated by a user clicking on a link to the pipeline in a document.